[2023-03-16 10:08:10,596] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:08:10,596] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:08:10,596] [INFO] DQC Reference Directory: /var/lib/cwl/stg36a26f2e-5e37-4ee8-afae-f7491e307d8f/dqc_reference
[2023-03-16 10:08:11,735] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:08:11,736] [INFO] Task started: Prodigal
[2023-03-16 10:08:11,736] [INFO] Running command: cat /var/lib/cwl/stg45d75546-7c25-4c24-9bdb-b4280310479b/OceanDNA-b28011.fa | prodigal -d OceanDNA-b28011/cds.fna -a OceanDNA-b28011/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:08:19,552] [INFO] Task succeeded: Prodigal
[2023-03-16 10:08:19,553] [INFO] Task started: HMMsearch
[2023-03-16 10:08:19,553] [INFO] Running command: hmmsearch --tblout OceanDNA-b28011/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36a26f2e-5e37-4ee8-afae-f7491e307d8f/dqc_reference/reference_markers.hmm OceanDNA-b28011/protein.faa > /dev/null
[2023-03-16 10:08:19,726] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:08:19,726] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg45d75546-7c25-4c24-9bdb-b4280310479b/OceanDNA-b28011.fa]
[2023-03-16 10:08:19,743] [INFO] Query marker FASTA was written to OceanDNA-b28011/markers.fasta
[2023-03-16 10:08:19,744] [INFO] Task started: Blastn
[2023-03-16 10:08:19,745] [INFO] Running command: blastn -query OceanDNA-b28011/markers.fasta -db /var/lib/cwl/stg36a26f2e-5e37-4ee8-afae-f7491e307d8f/dqc_reference/reference_markers.fasta -out OceanDNA-b28011/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:08:20,476] [INFO] Task succeeded: Blastn
[2023-03-16 10:08:20,477] [INFO] Selected 21 target genomes.
[2023-03-16 10:08:20,477] [INFO] Target genome list was writen to OceanDNA-b28011/target_genomes.txt
[2023-03-16 10:08:20,499] [INFO] Task started: fastANI
[2023-03-16 10:08:20,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg45d75546-7c25-4c24-9bdb-b4280310479b/OceanDNA-b28011.fa --refList OceanDNA-b28011/target_genomes.txt --output OceanDNA-b28011/fastani_result.tsv --threads 1
[2023-03-16 10:08:32,288] [INFO] Task succeeded: fastANI
[2023-03-16 10:08:32,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36a26f2e-5e37-4ee8-afae-f7491e307d8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:08:32,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36a26f2e-5e37-4ee8-afae-f7491e307d8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:08:32,334] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:08:32,334] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:08:32,334] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	77.4902	83	353	95	below_threshold
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	77.1656	60	353	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	77.1474	57	353	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	77.1474	57	353	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	77.0233	50	353	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.8423	53	353	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:08:32,336] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28011/tc_result.tsv
[2023-03-16 10:08:32,338] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:08:32,338] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:08:32,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36a26f2e-5e37-4ee8-afae-f7491e307d8f/dqc_reference/checkm_data
[2023-03-16 10:08:32,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:08:32,344] [INFO] Task started: CheckM
[2023-03-16 10:08:32,344] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28011/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28011/checkm_input OceanDNA-b28011/checkm_result
[2023-03-16 10:08:59,795] [INFO] Task succeeded: CheckM
[2023-03-16 10:08:59,796] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:08:59,798] [INFO] ===== Completeness check finished =====
[2023-03-16 10:08:59,798] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:08:59,799] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28011/markers.fasta)
[2023-03-16 10:08:59,800] [INFO] Task started: Blastn
[2023-03-16 10:08:59,800] [INFO] Running command: blastn -query OceanDNA-b28011/markers.fasta -db /var/lib/cwl/stg36a26f2e-5e37-4ee8-afae-f7491e307d8f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28011/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:09:00,836] [INFO] Task succeeded: Blastn
[2023-03-16 10:09:00,837] [INFO] Selected 11 target genomes.
[2023-03-16 10:09:00,837] [INFO] Target genome list was writen to OceanDNA-b28011/target_genomes_gtdb.txt
[2023-03-16 10:09:00,874] [INFO] Task started: fastANI
[2023-03-16 10:09:00,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg45d75546-7c25-4c24-9bdb-b4280310479b/OceanDNA-b28011.fa --refList OceanDNA-b28011/target_genomes_gtdb.txt --output OceanDNA-b28011/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:09:06,894] [INFO] Task succeeded: fastANI
[2023-03-16 10:09:06,901] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:09:06,901] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_018647275.1	s__Ascidiaceihabitans sp018647275	98.5292	255	353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002478745.1	s__Ascidiaceihabitans sp002478745	93.5984	300	353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.75	99.75	0.89	0.89	2	-
GCA_905182105.1	s__Ascidiaceihabitans sp905182105	88.901	306	353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182355.1	s__Ascidiaceihabitans sp905182355	78.813	162	353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302465.1	s__Ascidiaceihabitans donghaensis	77.4902	83	353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622405.1	s__Sulfitobacter donghicola	77.1474	57	353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000622325.1	s__Sulfitobacter geojensis	77.0233	50	353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_013282155.1	s__Sulfitobacter sp013282155	76.9069	56	353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCA_013139555.1	s__Sulfitobacter sp013139555	76.8489	51	353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352065.1	s__Sulfitobacter sp003352065	76.701	50	353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:09:06,903] [INFO] GTDB search result was written to OceanDNA-b28011/result_gtdb.tsv
[2023-03-16 10:09:06,907] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:09:06,911] [INFO] DFAST_QC result json was written to OceanDNA-b28011/dqc_result.json
[2023-03-16 10:09:06,911] [INFO] DFAST_QC completed!
[2023-03-16 10:09:06,911] [INFO] Total running time: 0h0m56s